<tool id="pe_sync" name="pe-sync: Paired-end synchronization check" version="1.0">
  <description>The Paired-end synchronization check program determines if the reads in paired-end fastq files are in the proper order (synchronized).</description>
  <command interpreter="perl">
    pe_sync_2_files.pl $quickcheck $input1 $input2 2>&amp;1 | tee $output
  </command>
  <inputs>
    <param name="input1" type="data" format="fastq" label="Input 1"/>
    <param name="input2" type="data" format="fastq" label="Input 2"/>
    <param name="quickcheck" type="boolean" truevalue="quick" falsevalue="" checked="false" label="Just check a sample of the sequences"
           help=""/>
  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal"   description="Bad input dataset" />
  </stdio>
  <outputs>
    <data format="txt" name="output" label="pe-sync report for ${input1.name} and ${input2.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
      <param name="input2" ftype="fastq" value="reads2.fastqsanger" />
      <param name="quickcheck" value="false"/>
      <output name="output">
        <assert_contents>
            <has_text text="PASSED" />
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
      <param name="input2" ftype="fastq" value="reads_unsync_2.fastqsanger" />
      <param name="quickcheck" value="false"/>
      <output name="output">
        <assert_contents>
            <has_text text="FAILED" />
        </assert_contents>
      </output>
    </test>

  </tests>
  <help>
Paired-end read file synchronization checks if left and right reads are in the same order.

The "quick" option will not report the percent of out-of-sync reads
for many failed files, but will run much faster.

This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids.
Other types of read ID formats may cause a terminal error. 

  </help>
</tool>